• ordered by machine, using only LSR for remaining

• ordered by machine, using only LSR for remaining

• median value of markers in each cluster

• median z-score of markers in each cluster

• median z-score of markers in each cluster

• median z-score of markers in each cluster

##   Running PhenoGraph...  Finding nearest neighbors...DONE ~ 0.072 s
##   Compute jaccard coefficient between nearest-neighbor sets...DONE ~ 1.473 s
##   Build undirected graph from the weighted links...DONE ~ 0.241 s
##   Run louvain clustering on the graph ...DONE ~ 0.113 s
##   Return a community class
##   -Modularity value: 0.9052814 
##   -Number of clusters: 16 DONE!

##   Running t-SNE...with seed 42  DONE

• colored by “meta” phenograph cluster

• colored by control

• colored by percent of cells that are naive in original clusters

• colored by percent of cells that are effector in original clusters

• colored by percent of cells that are effector memory in original clusters

• colored by percent of cells that are central memory in original clusters

• colored by median CD45 (scaled) expression in original clusters

• colored by median CCR7 (scaled) expression in original clusters

• colored by median CD28 (scaled) expression in original clusters

• colored by median CD95 (scaled) expression in original clusters

• colored by median CD27 (scaled) expression in original clusters

• colored by median IgD (scaled) expression in original clusters

• colored by median CD19 (scaled) expression in original clusters

• meta-clusters 9, 2, 1, 16, 8

• meta-clusters 9, 2, 1, 16, 8

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729477/

The total T cells (CD3+), helper T cells (CD3+CD4+), and total B cells (CD19+) were gated. The expression of mIgD on T and B cells was analyzed by calculating the percentages of CD3+IgD+, CD3+CD4+IgD+, immature B cells (CD19+IgM+IgD-) and mature B cells (CD19+IgD+) on a flow cytometer (model FC 500; Beckman Coulter Ltd., USA)

https://www.ncbi.nlm.nih.gov/pubmed/11243700

• IgD values ~ 100 not really positive
• see https://github.com/PankratzLab/auto-fcs/issues/64
• higher CD19 not too weird on LSR